FMO DATABASE

FMODB ID: K35Y3

Calculation Name: 2YAD-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YAD

Chain ID: D

ChEMBL ID:

UniProt ID: P11686

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-497047.598793
FMO2-HF: Nuclear repulsion	465455.884311
FMO2-HF: Total energy	-31591.714482
FMO2-MP2: Total energy	-31679.524663

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(D:88:LEU)

Summations of interaction energy for fragment #1(D:88:LEU)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-1.9949319973733E-17	1.233	-0.012	-0.484	-0.738	0.002

Interaction energy analysis for fragmet #1(D:88:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.013

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	D	90	THR	0	-0.006	0.000	3.857	-0.719	0.514	-0.012	-0.484	-0.738	0.002
4	D	91	THR	0	0.023	-0.003	6.330	0.362	0.362	0.000	0.000	0.000	0.000
5	D	92	ALA	0	-0.040	-0.011	9.411	-0.141	-0.141	0.000	0.000	0.000	0.000
6	D	93	THR	0	-0.020	0.001	12.228	0.047	0.047	0.000	0.000	0.000	0.000
7	D	94	PHE	0	0.003	0.000	13.606	0.002	0.002	0.000	0.000	0.000	0.000
8	D	95	SER	0	0.027	0.016	18.771	-0.008	-0.008	0.000	0.000	0.000	0.000
9	D	96	ILE	0	-0.028	-0.023	21.936	0.014	0.014	0.000	0.000	0.000	0.000
10	D	97	GLY	0	0.011	0.015	24.916	-0.005	-0.005	0.000	0.000	0.000	0.000
11	D	98	SER	0	0.011	-0.002	28.044	-0.003	-0.003	0.000	0.000	0.000	0.000
12	D	99	THR	0	-0.053	-0.041	28.810	-0.005	-0.005	0.000	0.000	0.000	0.000
13	D	100	GLY	0	0.020	0.034	26.481	-0.006	-0.006	0.000	0.000	0.000	0.000
14	D	101	LEU	0	-0.027	-0.013	21.643	-0.007	-0.007	0.000	0.000	0.000	0.000
15	D	102	VAL	0	0.006	-0.005	17.953	0.012	0.012	0.000	0.000	0.000	0.000
16	D	103	VAL	0	-0.006	-0.005	14.463	-0.030	-0.030	0.000	0.000	0.000	0.000
17	D	104	TYR	0	-0.058	-0.046	13.022	0.024	0.024	0.000	0.000	0.000	0.000
18	D	105	ASP	-1	-0.829	-0.927	11.074	-0.230	-0.230	0.000	0.000	0.000	0.000
19	D	106	TYR	0	0.023	-0.019	8.093	0.070	0.070	0.000	0.000	0.000	0.000
20	D	107	GLN	0	-0.043	0.002	6.355	0.119	0.119	0.000	0.000	0.000	0.000
21	D	108	GLN	0	-0.002	-0.013	8.726	0.097	0.097	0.000	0.000	0.000	0.000
22	D	109	LEU	0	0.008	0.011	11.916	-0.015	-0.015	0.000	0.000	0.000	0.000
23	D	110	LEU	0	-0.019	-0.003	13.790	-0.025	-0.025	0.000	0.000	0.000	0.000
24	D	111	ILE	0	0.023	0.018	15.174	-0.001	-0.001	0.000	0.000	0.000	0.000
25	D	112	ALA	0	-0.009	0.006	17.892	-0.001	-0.001	0.000	0.000	0.000	0.000
26	D	113	TYR	0	-0.003	-0.013	20.147	-0.007	-0.007	0.000	0.000	0.000	0.000
27	D	114	LYS	1	0.912	0.958	23.013	0.075	0.075	0.000	0.000	0.000	0.000
28	D	115	PRO	0	0.025	0.021	25.296	-0.004	-0.004	0.000	0.000	0.000	0.000
29	D	116	ALA	0	0.055	0.030	28.463	-0.001	-0.001	0.000	0.000	0.000	0.000
30	D	117	PRO	0	-0.007	-0.009	28.412	-0.002	-0.002	0.000	0.000	0.000	0.000
31	D	118	GLY	0	0.022	0.015	29.550	0.005	0.005	0.000	0.000	0.000	0.000
32	D	119	THR	0	-0.004	-0.007	30.127	0.005	0.005	0.000	0.000	0.000	0.000
33	D	148	CYS	0	-0.074	-0.023	29.161	-0.004	-0.004	0.000	0.000	0.000	0.000
34	D	121	CYS	0	-0.078	-0.050	21.077	0.011	0.011	0.000	0.000	0.000	0.000
35	D	122	TYR	0	0.059	0.039	25.181	0.004	0.004	0.000	0.000	0.000	0.000
36	D	123	ILE	0	-0.023	-0.015	20.402	-0.003	-0.003	0.000	0.000	0.000	0.000
37	D	124	MET	0	-0.001	0.013	20.930	0.017	0.017	0.000	0.000	0.000	0.000
38	D	125	LYS	1	0.861	0.921	16.443	-0.129	-0.129	0.000	0.000	0.000	0.000
39	D	126	ILE	0	-0.054	-0.024	14.190	-0.005	-0.005	0.000	0.000	0.000	0.000
40	D	127	ALA	0	0.021	0.017	17.085	0.004	0.004	0.000	0.000	0.000	0.000
41	D	128	PRO	0	-0.007	-0.017	13.979	0.008	0.008	0.000	0.000	0.000	0.000
42	D	129	GLU	-1	-0.877	-0.935	13.795	0.668	0.668	0.000	0.000	0.000	0.000
43	D	130	SER	0	-0.077	-0.048	16.295	-0.023	-0.023	0.000	0.000	0.000	0.000
44	D	131	ILE	0	0.023	0.018	11.635	-0.063	-0.063	0.000	0.000	0.000	0.000
45	D	132	PRO	0	-0.021	0.007	15.930	-0.002	-0.002	0.000	0.000	0.000	0.000
46	D	133	SER	0	0.084	0.035	17.553	-0.009	-0.009	0.000	0.000	0.000	0.000
47	D	134	LEU	0	0.099	0.038	18.669	-0.009	-0.009	0.000	0.000	0.000	0.000
48	D	135	GLU	-1	-0.821	-0.891	20.160	0.052	0.052	0.000	0.000	0.000	0.000
49	D	136	ALA	0	-0.023	-0.004	21.599	-0.009	-0.009	0.000	0.000	0.000	0.000
50	D	137	LEU	0	-0.003	0.008	19.646	-0.008	-0.008	0.000	0.000	0.000	0.000
51	D	138	THR	0	0.013	-0.009	22.937	-0.015	-0.015	0.000	0.000	0.000	0.000
52	D	139	ARG	1	0.850	0.903	25.775	-0.076	-0.076	0.000	0.000	0.000	0.000
53	D	140	LYS	1	0.913	0.964	23.086	-0.112	-0.112	0.000	0.000	0.000	0.000
54	D	141	VAL	0	0.018	-0.013	25.255	-0.004	-0.004	0.000	0.000	0.000	0.000
55	D	142	HIS	0	0.019	0.029	27.940	-0.007	-0.007	0.000	0.000	0.000	0.000
56	D	143	ASN	0	-0.038	-0.036	30.071	-0.007	-0.007	0.000	0.000	0.000	0.000
57	D	144	PHE	0	-0.064	-0.044	28.149	0.003	0.003	0.000	0.000	0.000	0.000
58	D	145	GLN	0	-0.005	0.026	31.404	-0.006	-0.006	0.000	0.000	0.000	0.000
59	D	146	MET	0	-0.084	-0.022	25.815	-0.004	-0.004	0.000	0.000	0.000	0.000
60	D	147	GLU	-1	-0.905	-0.970	30.310	0.011	0.011	0.000	0.000	0.000	0.000
61	D	180	PHE	0	0.050	0.018	15.088	-0.003	-0.003	0.000	0.000	0.000	0.000
62	D	181	LEU	0	-0.026	-0.025	17.201	0.012	0.012	0.000	0.000	0.000	0.000
63	D	182	GLY	0	0.079	0.052	14.117	-0.008	-0.008	0.000	0.000	0.000	0.000
64	D	183	MET	0	0.022	0.007	13.358	0.035	0.035	0.000	0.000	0.000	0.000
65	D	184	ALA	0	0.015	0.022	13.173	0.029	0.029	0.000	0.000	0.000	0.000
66	D	185	VAL	0	0.059	0.028	15.111	0.029	0.029	0.000	0.000	0.000	0.000
67	D	186	SER	0	-0.009	-0.021	17.636	0.027	0.027	0.000	0.000	0.000	0.000
68	D	187	THR	0	-0.054	-0.035	17.637	0.010	0.010	0.000	0.000	0.000	0.000
69	D	188	LEU	0	-0.011	0.005	19.296	0.014	0.014	0.000	0.000	0.000	0.000
70	D	190	GLY	0	0.036	0.039	23.131	0.010	0.010	0.000	0.000	0.000	0.000
71	D	191	GLU	-1	-0.959	-0.988	24.822	-0.076	-0.076	0.000	0.000	0.000	0.000
72	D	192	VAL	0	-0.046	-0.004	26.608	0.006	0.006	0.000	0.000	0.000	0.000
73	D	193	PRO	0	-0.009	-0.002	28.013	-0.001	-0.001	0.000	0.000	0.000	0.000
74	D	194	LEU	0	-0.003	-0.003	23.851	0.000	0.000	0.000	0.000	0.000	0.000
75	D	195	TYR	0	0.006	-0.007	27.215	0.004	0.004	0.000	0.000	0.000	0.000
76	D	196	TYR	0	0.025	0.011	22.411	0.001	0.001	0.000	0.000	0.000	0.000
77	D	197	ILE	0	-0.017	-0.010	24.937	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:88:LEU)